From 441dba0d75055fcbf2f75e6ca43754b9b0facc70 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Mon, 31 Jul 2023 13:17:04 -0400 Subject: [PATCH 1/4] Update to core 2.16.1, tiledb-py 0.22.1, tiledb-r 0.20.2, and somacore 1.0.4 --- apis/python/setup.py | 2 +- apis/r/tools/get_tarball.R | 4 +-- .../cmake/Modules/FindTileDB_EP.cmake | 28 +++++++++---------- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/apis/python/setup.py b/apis/python/setup.py index 9c5021400d..49285918e9 100644 --- a/apis/python/setup.py +++ b/apis/python/setup.py @@ -291,7 +291,7 @@ def run(self): "scanpy>=1.9.2", "scipy", "somacore==1.0.4", - "tiledb~=0.22.0", + "tiledb~=0.22.1", "typing-extensions", # Note "-" even though `import typing_extensions` ], extras_require={ diff --git a/apis/r/tools/get_tarball.R b/apis/r/tools/get_tarball.R index 97ab7f371e..9ce4d3337a 100644 --- a/apis/r/tools/get_tarball.R +++ b/apis/r/tools/get_tarball.R @@ -1,8 +1,8 @@ #!/usr/bin/env Rscript ## version pinning info -tiledb_core_version <- "2.16.0" -tiledb_core_sha1 <- "d682dd0" +tiledb_core_version <- "2.16.1" +tiledb_core_sha1 <- "3abc68f" if ( ! dir.exists("inst/") ) { stop("No 'inst/' directory. Exiting.", call. = FALSE) diff --git a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake b/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake index 07172299da..033b7a0b3f 100644 --- a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake +++ b/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake @@ -58,8 +58,8 @@ else() # NB When updating the pinned URLs here, please also update in file apis/r/tools/get_tarball.R if(DOWNLOAD_TILEDB_PREBUILT) if (WIN32) # Windows - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.0/tiledb-windows-x86_64-2.16.0-d682dd0.zip") - SET(DOWNLOAD_SHA1 "82a79fda3daecc46ae24c86a328e52184460dabe") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.1/tiledb-windows-x86_64-2.16.1-3abc68f.zip") + SET(DOWNLOAD_SHA1 "3bc7d9f88f67b1138dd23a4b99a22a7b16ebf74f") elseif(APPLE) # OSX # Status quo as of 2023-05-18: @@ -76,22 +76,22 @@ else() # o CMAKE_SYSTEM_PROCESSOR is x86_64 if (CMAKE_OSX_ARCHITECTURES STREQUAL x86_64) - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.0/tiledb-macos-x86_64-2.16.0-d682dd0.tar.gz") - SET(DOWNLOAD_SHA1 "d7b22fa3cb9cbe131734d9f18beb3362908aeccf") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.1/tiledb-macos-x86_64-2.16.1-3abc68f.tar.gz") + SET(DOWNLOAD_SHA1 "a0f322d7169635065e2117feac6cc1725e5c97cb") elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64) - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.0/tiledb-macos-arm64-2.16.0-d682dd0.tar.gz") - SET(DOWNLOAD_SHA1 "09c62e3211e5277263c1545d74d698d450ebcb77") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.1/tiledb-macos-arm64-2.16.1-3abc68f.tar.gz") + SET(DOWNLOAD_SHA1 "e2ad15187561c72169ad998183d8d65984ad0f03") elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)") - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.0/tiledb-macos-x86_64-2.16.0-d682dd0.tar.gz") - SET(DOWNLOAD_SHA1 "d7b22fa3cb9cbe131734d9f18beb3362908aeccf") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.1/tiledb-macos-x86_64-2.16.1-3abc68f.tar.gz") + SET(DOWNLOAD_SHA1 "a0f322d7169635065e2117feac6cc1725e5c97cb") elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm") - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.0/tiledb-macos-arm64-2.16.0-d682dd0.tar.gz") - SET(DOWNLOAD_SHA1 "09c62e3211e5277263c1545d74d698d450ebcb77") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.1/tiledb-macos-arm64-2.16.1-3abc68f.tar.gz") + SET(DOWNLOAD_SHA1 "e2ad15187561c72169ad998183d8d65984ad0f03") endif() else() # Linux - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.0/tiledb-linux-x86_64-2.16.0-d682dd0.tar.gz") - SET(DOWNLOAD_SHA1 "be0bfd5512c159b960988a4bd41366e9f020115f") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.1/tiledb-linux-x86_64-2.16.1-3abc68f.tar.gz") + SET(DOWNLOAD_SHA1 "0d65d8a1c0766dec3a5a76e72419850b76c955b7") endif() ExternalProject_Add(ep_tiledb @@ -113,8 +113,8 @@ else() else() # Build from source ExternalProject_Add(ep_tiledb PREFIX "externals" - URL "https://github.com/TileDB-Inc/TileDB/archive/2.16.0.zip" - URL_HASH SHA1=c2779f931c84d931e5fca6dc3a858e66fc542276 + URL "https://github.com/TileDB-Inc/TileDB/archive/2.16.1.zip" + URL_HASH SHA1=da077ef3970a3e48a2bb28f35c45d5775b6f7c9e DOWNLOAD_NAME "tiledb.zip" CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX} From 862af179b385bfe181caa8dafcd5473a2ad22182 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Mon, 31 Jul 2023 14:38:47 -0400 Subject: [PATCH 2/4] Put somacore 1.0.4 on #1553 --- .pre-commit-config.yaml | 2 +- apis/python/setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b9d799b64c..1c57d54fea 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ repos: - id: mypy additional_dependencies: - "pandas-stubs==1.5.3.230214" - - "somacore==1.0.4" + - "somacore==1.0.3" - "types-setuptools==67.4.0.3" args: ["--config-file=apis/python/pyproject.toml", "apis/python/src", "apis/python/devtools"] pass_filenames: false diff --git a/apis/python/setup.py b/apis/python/setup.py index 49285918e9..ad226dfec5 100644 --- a/apis/python/setup.py +++ b/apis/python/setup.py @@ -290,7 +290,7 @@ def run(self): "pyarrow>=9.0.0", "scanpy>=1.9.2", "scipy", - "somacore==1.0.4", + "somacore==1.0.3", "tiledb~=0.22.1", "typing-extensions", # Note "-" even though `import typing_extensions` ], From 650b2fc9844fb2e78f31cbce89ff11a7f94f4a54 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Mon, 31 Jul 2023 15:22:20 -0400 Subject: [PATCH 3/4] apis/r/NEWS.md --- apis/r/NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apis/r/NEWS.md b/apis/r/NEWS.md index 832ae4b38f..a11f2e7fb0 100644 --- a/apis/r/NEWS.md +++ b/apis/r/NEWS.md @@ -1,4 +1,4 @@ -# tiledbsoma 0.0.0.* +# tiledbsoma 1.4.* ## Changes From d8b4c3360401c4b596905922603321a132c0e941 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Wed, 2 Aug 2023 18:35:22 -0400 Subject: [PATCH 4/4] split out R-versioning mods to another PR --- .pre-commit-config.yaml | 2 +- apis/python/setup.py | 2 +- apis/r/NEWS.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1c57d54fea..b9d799b64c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ repos: - id: mypy additional_dependencies: - "pandas-stubs==1.5.3.230214" - - "somacore==1.0.3" + - "somacore==1.0.4" - "types-setuptools==67.4.0.3" args: ["--config-file=apis/python/pyproject.toml", "apis/python/src", "apis/python/devtools"] pass_filenames: false diff --git a/apis/python/setup.py b/apis/python/setup.py index ad226dfec5..49285918e9 100644 --- a/apis/python/setup.py +++ b/apis/python/setup.py @@ -290,7 +290,7 @@ def run(self): "pyarrow>=9.0.0", "scanpy>=1.9.2", "scipy", - "somacore==1.0.3", + "somacore==1.0.4", "tiledb~=0.22.1", "typing-extensions", # Note "-" even though `import typing_extensions` ], diff --git a/apis/r/NEWS.md b/apis/r/NEWS.md index a11f2e7fb0..832ae4b38f 100644 --- a/apis/r/NEWS.md +++ b/apis/r/NEWS.md @@ -1,4 +1,4 @@ -# tiledbsoma 1.4.* +# tiledbsoma 0.0.0.* ## Changes